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Table 4 Comparison of PPV = TP/(TP+FP) in promoter predictions using the annotated TSS sites.

From: Prediction of regulatory elements in mammalian genomes using chromatin signatures

Untreated

 

Total Prediction (TP+FP)

TP

PPV

p-value

Heintzman et al.

198

181

91.41%

< 1.0 × 10-16

HMM(c1 = 2.205)

198

189

95.45%

< 1.0 × 10-16

HMM (c1 = 1.6)

256

234

91.41%

< 1.0 × 10-16

HMM (c1 = 0.5)

337

264

78.34%

< 1.0 × 10-16

Treated

 

Total Prediction (TP+FP)

TP

PPV

p-value

Heintzman et al.

207

183

88.41%

< 1.0 × 10-16

HMM (c1 = 2.1)

207

196

94.69%

< 1.0 × 10-16

HMM (c1 = 1.367)

279

247

88.50%

2.8 × 10-3

HMM (c1 = 0.5)

362

278

76.80%

< 1.0 × 10-16

  1. We calculated p value by generating random predictions on the ENCODE regions.
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BMC Bioinformatics

ISSN: 1471-2105

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